I want to perform molecular dynamics simulations of 2qv4 using charrm36-2022. However, 2qv4 contains the PYROGLUTAMIC ACID which is a non-standard residue and is not recognized by the force field (pdb2gmx).
I would really appreciate any suggestions of how I should proceed in order to setup the system. Do I need to parametrize the pyroglutamate (PCA) o should I use the same parameters of glutamine and introduce a new residue in the force field…
I have exactly the same problem, tried many ways, and none of the worked! Hopefully somebody knows what to do. It hurts when you see only for one residue you have such a painful problem!
The followings worked for me several years ago.
If you are not restricted to use the CHARMM ff, then use one of the AMBER ff and translate the PCA paramters from any of the TINKER prm files. Of course you have to add the residue types and also add PCA residue to the hdb file.
The answer is beyond the length (and time) of a mailing list advice/suggestions. Nevertheless, start with the gromacs manual and learn how paramter files are buil and organized.